Contribution of non-coding mutations to RPGRIP1-mediated inherited retinal degeneration.

Purpose: With the advent of gene therapies for inherited retinal degenerations (IRDs), genetic diagnostics will have an increasing role in clinical decision making. Yet the genetic cause of disease cannot be identified using exon based sequencing for a significant portion of patients. We hypothesized that noncoding mutations contribute significantly to the genetic causality of IRDs and evaluated patients with single coding mutations in RPGRIP1 to test this hypothesis. Methods: IRD families underwent targeted panel sequencing. Unsolved cases were explored by whole exome and genome sequencing looking for additional mutations. Candidate mutations were then validated by Sanger sequencing, quantitative PCR, and in vitro splicing assays in two cell lines analyzed through amplicon sequencing. Results: Among 1722 families, three had biallelic loss of function mutations in RPGRIP1 while seven had a single disruptive coding mutation. Whole exome and genome sequencing revealed potential noncoding mutations in these seven families. In six, the noncoding mutations were shown to lead to loss of function in vitro. Conclusion: Noncoding mutations were identified in 6 of 7 families with single coding mutations in RPGRIP1. The results suggest that noncoding mutations contribute significantly to the genetic causality of IRDs and RPGRIP1 mediated IRDs are more common than previously thought.